A multigene phylogeny of the Dothideomycetes using four nuclear loci

Schoch, Conrad L.; Shoemaker, R. A.; Seifert, Keith A.; Hambleton, Sarah; Spatafora, Joseph W.; Crous, Pedro W.

doi:10.3852/mycologia.98.6.1041

Cited by 252 publications

(66 citation statements)

References 40 publications

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“…CO27-5 v1.0 (Wu et al 2017), Neurospora crassa OR74A v2.0 (Galagan et al 2003), Lecythophora sp. AK0013 v1.0 (Damm et al 2010; U’Ren et al 2012), Botryosphaeria dothidea (Slippers et al 2004; Desprez-Loustau et al 2006; Schoch et al 2006; Slippers and Wingfield 2007; Piškur et al 2011), Fusarium oxysporum sp. lycopersici 4287 v2 (Ma et al 2010) with available annotated genomes were retrieved from the JGI (Joint Genome Institute) MycoCosm database.…”

Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

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Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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“…Members of Phaeosphaeriaceae can be endophytic, epiphytic, saprobic, or pathogenic on plants with many species and their asexual morphs causing serious diseases of crops worldwide (Shoemaker & Babcock 1989, Schoch et al 2006, Hyde et al 2013. Barr (1979) introduced Phaeosphaeriaceae with Phaeosphaeria as the type genus and described the family as saprobic, pathogenic or hyperparasitic.…”

Section: Introductionmentioning

confidence: 99%

“…Phaeosphaeriaceae is a large and important family of Pleosporales, in the suborder Pleosporineae, Dothideomycetes (Câmara et al 2002, Kodsueb et al 2006, Schoch et al 2006, Gruyter et al 2010, Hyde et al 2013. Members of Phaeosphaeriaceae can be endophytic, epiphytic, saprobic, or pathogenic on plants with many species and their asexual morphs causing serious diseases of crops worldwide (Shoemaker & Babcock 1989, Schoch et al 2006, Hyde et al 2013.…”

Section: Introductionmentioning

confidence: 99%

The sexual state of Setophoma

Phookamsak¹,

Liu²,

Manamgoda³

et al. 2014

Phytotaxa

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A sexual state of Setophoma, a coelomycete genus of Phaeosphaeriaceae, was found causing leaf spots of sugarcane (Saccharum officinarum). Pure cultures from single ascospores produced the asexual morph on rice straw and bamboo pieces on water agar. Multiple gene phylogenetic analysis using ITS, LSU and RPB2 showed that our strains belong to the family Phaeosphaeriaceae. The strains clustered with Setophoma sacchari with strong support (100% ML, 100% MP and 1.00 PP) and formed a well-supported clade with other Setophoma species. Therefore our strains are identified as S. sacchari. In this paper descriptions and photographs of the sexual and asexual morphs of S. sacchari are provided. The sexual state of S. sacchari is compared with Leptosphaeria sacchari, L. saccharicola, Phaeosphaeria nodorum and Sphaerulina sacchari which have similar morphological characters; however they differ in size and colour of ascospores and in the characters of the asexual state. Setophoma is clearly separated from other Phaeosphaeria species based on the phylogenetic analysis.

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“…Lumbsch & Lindemuth (2001) used LSU and SSU gene data to analyze the major lineages of Dothideomycetes in which the Myriangium species were included in the order Myriangiales. Schoch et al (2006) used M. duriaei and four Elsinoe spp. in their phylogenetic analyses and found that these Elsinoe species belong to a different family, Elsinoaceae.…”

Section: Taxonomymentioning

confidence: 99%

The status of Myriangiaceae (Dothideomycetes)

Dissanayake¹,

Jayawardena²,

Boonmee³

et al. 2014

Phytotaxa

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The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, "Sphaceloma"-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

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A multigene phylogeny of the Dothideomycetes using four nuclear loci

Cited by 252 publications

References 40 publications

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

The sexual state of Setophoma

The status of Myriangiaceae (Dothideomycetes)

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